SilverCollection - Web Portal for Biological Collections

We are please to announce we will be attending BOTANY 2010 this year. Being the year of biodiversity we decided to also perform an experiment & case study by volunteering to image herbarium specimens before and after the conference along the east coast. This year the conference will be held in Providence, Rhode Island on July 31 - August 4 at the Rhode Island Convention Center. More information about the conference can be found on the official website.

Imaging Tour

SilverBiology will be performing full day imaging and demonstrations of our software.  We will be leaving from our office in Baton Rouge on July 18th and driving to Botany 2010 (BSA Conference in Providence, Rhode Island).  We will be passing through the east coast until August 15th.  During this time we would like to stop and provide a one day workshop on imaging, processing, and interacting with herbarium specimen sheets.  Our goal during this tour is to image and process over 5,000 specimen sheets then present that information online in our newest version of our SilverCollection web portal.  We are asking for interested herbaria to request that we stop and visit by sending us an email at contact@silverbiology.com.

For complete details on the project please visit: http://botany2010.silverbiology.com/

As we attend more conferences and start new projects it is important for us to know what we have done and what we plan on doing for the future.  We feel that it is important to know the history of a company and also give you a chance to see our schedule in the near future.  With that being said we put together a new web page on our website called Timeline.  This web page shows everything about our company in an interactive timeline tool.

We will continue to update the timeline with new projects and events and hope that you enjoy this new feature on our website.  Link to the SilverBiology Timeline

After a wonderful week in Montpellier, France and listening to some very interesting talks it’s time to get back to the daily grind and continue our developments. Before we do, I wanted to recap on some of the activities SilverBiology was involved in.

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Another session of Nomina has been concluded.  EOL was nice enough to again host this workshop at the Marine Biological Laboratory in Woods Hole.  This time the focus was on methods for reconciling heterogeneous taxonomic data.  The group this time was made up of myself from SilverBiology, GBif, EOL, and Atlas of Living Australia (ALA).

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SilverBiology will be exhibiting again this year at the SPNHC 2009.  The conference is to take place on July 6th - 11th, 2009 in Leiden, Netherlands.

Bridging Continents presents new, large-scaled infrastructure projects in natural history collections, the state-of-art in collection care and best practice, the latest on digitization of collections and much more. http://www.spnhc2009.org

We will be showcasing our newest version of SilverCollection, our web portal for biological collections.  We have a new api and some great new features we are excited to show off.

We have also been doing research in fuzzy matching for scientific names and will be showing how TAXAMATCH web service can be used to help with scientific literature.

If your museum has an Arthropod, Herbarium, or other start to a digital collection we really want to speak with you during the meeting. We have some additional tools coming out this year that should help with imaging and processing scientific data.

We strive to build good working relationships with museums to improve our software, create open source tools, and offer custom solutions to your specific needs.

See you there!

Last week was the fourth gathering for Nomina.  These meetings have been created by EOL & GBIF in collaboration with BHL (Biodiverstiy Heritage Library).  The goal for this meeting was to improve Taxonomic Name Recognition, discover the tools and algorithms that are currently being used and how to merge and improve what we are currently doing to make things faster and better.  With over 35,000 books and more then 14 million scientific pages from the BHL it is important to provide the most accurate tools to help discover information from the past.

The workspace used for this meeting includes links to web applications, source code, shared dictionaries, test files, and other useful resources for those in need of tools and services for finding, parsing, and processing taxonomic names. http://code.google.com/p/taxon-name-processing

The meeting was very productive and as changes and improvements are made to the individual projects the overall goals will be one step closer.

SilverBiology’s purpose at this meeting was to demonstrate and see how our TAXAMATCH web service can be used with fuzzy matching on scientific names that are misspelled.  Our goal is to implement this with the Global Names Index (globalnames.org) and GBIF’s species checklist.  These will be public web services so anyone can use to search for scientific names.

TAXAMATCH was originally developed by Tony Rees at OBIS and developed in PL/SQL.  Our open source version is a PHP/MySql implementation of the algorithm with a few additional configurations.  To learn more about Tony’s project and the continuation of our project just follow the links below.

Original TAXAMATCH: http://www.cmar.csiro.au/datacentre/taxamatch.htm
Our web service version: http://taxamatch.silverbiology.com (IN DEVELOPMENT)

If you would like to see more about the past Nomina workshops you can find them here:

Nomina 4: http://hickory.eol.org:8081/display/public/Nomina+IV
Nomina 2: http://blog.eol.org/2008/04/24/nomina-2-workshop-succeeded

SilverBiology is pleased to announce the expansion of our company to the European Universities and Museums to support their biological collections. Our new office is located in Sevilla, Spain.  At the moment we are looking at the current status of collections and will be introducing ourselves to many of the universities in the near future.

We are excited to introduce Maciej Wyszkowski to our team.  He is the European Regional Manager of SilverBiology and will be overseeing the biodiversity needs in this part of the world.  If you are interested in speaking with him on how SilverCollection, our web portal for scientific collections, can work with your collection please contact us now. To view a full list of all our current services please visit: http://www.silverbiology.com/products

You are also welcome to discuss any projects that you need help with or integrating with current standards and technologies.  Our focus is to provide open source and licensed based software tools to provide solutions for scientific goals throughout the world.

You may contact us at: http://www.silverbiology.com/company/contactus.php

We will be attending the SPNHC2009 (6 - 11 July 2009, Leiden, The Netherlands). You can also find out about our future events at: http://www.silverbiology.com/company/events.html

I am pleased to announce that SilverBiology has accepted the task of building a Php Port of Tony Rees’ Taxamatch (http://www.cmar.csiro.au/datacentre/taxamatch.htm). TAXAMATCH is a “fuzzy” matching algorithm for taxon names and potential applications in taxonomic databases developed by Tony Rees at the CSIRO Marine and Atmospheric Research in Australia.

SilverBiology’s initial interest in providing an API service is in anticipation for our upcoming product called “SilverArchive” (http://www.silverbiology.com/products/silverarchive), where we help process herbarium specimen data using a human distribution model approach.  Having this tool to accurately spell check for scientific names will be highly useful for the efficiency of our software and our clients.  Our other goal is to provide services to easily inspect and clean scientific names.

This web service is an open source project and is being developed to allow unique computer aided solutions for a variety of applications.  The API will be a RESTful service that will initially support the JSON format.  We hope to extend this to XML and other requested formats.

You can find more about our project at: http://taxamatch.silverbiology.com as we continue to develop this service.  The project’s source code is located at: http://code.google.com/p/taxamatch-webservice.  If anyone is interested in testing this service and getting involved or would like to use this service when it is completed, we would love to hear from you.  Our goal is to build a service that is useful for everyone so all types of input is welcome.

This project is still in progress so no release date has been set.  We are hoping to have an Alpha release, in May 2009, with some real world examples of using the system.  We will post additional announcements as we progress with this service.  Anyone that is interested in getting involved please contact Mike Giddens (mikegiddens <at> silverbiology.com)

We want to thank David Remsen and everyone else that has already contacted us about testing and using the service.  The more initial tests and uses we come up with the better the service will become.

Regards,

Michael Giddens

SilverBiology is proud to announce that they have been selected by CyberFlora Louisiana to design, manage, develop, and provide technical guidance on the digitization of more then 1 million herbarium specimen sheets.  SilverCollection will be the official web portal for the herbarium collections in Louisiana.

SilverCollection is a webportal for biological collections and will be the primary interface to over 1.3 million herbarium specimens.  There will be custom features designed to focus on the CyberFlora project goals and a highly useful “api/web service” to interact with the data.

SilverBiology will be also introducing new software products this year in conjunction with the Cyberflora project.  Our goal is to develop new tools during the development of the Louisiana Herbarium Database to show as a model and ways for other consortia can follow.

This is a big endeavor and our team is excited to be working with Cyberflora Louisiana.

To find out more about the project you can monitor the official Cyberflora Louisiana Blog at: http://news.cyberfloralouisiana.com

Have you ever been doing field research, had your GPS, and searched for a locality or species? Well, what happens when you find and record the coordinates then later have no idea which county you where in?

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